TB-Profiler result

Run: SRR4033377
Summary

Run ID: SRR4033377

Sample name:

Date: 04-04-2023 06:03:10

Number of reads: 1534393

Percentage reads mapped: 99.45

Strain: lineage2.2.1

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.97
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.95
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.97
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
katG 2155630 p.Trp161* stop_gained 0.18 isoniazid
katG 2155683 c.428delA frameshift_variant 0.14 isoniazid
thyA 3074365 p.Tyr36Cys missense_variant 0.11 para-aminosalicylic_acid
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 5965 c.726A>T synonymous_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7700 c.399G>A synonymous_variant 0.15
gyrA 8286 p.Asn329Tyr missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491790 c.1008C>T synonymous_variant 0.18
mshA 575907 p.Ala187Val missense_variant 0.92
mshA 576571 c.1224G>A synonymous_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 0.93
rpoB 761222 c.1416G>A synonymous_variant 0.13
rpoB 761281 p.Gly492Asp missense_variant 0.14
rpoB 761295 p.Tyr497Asn missense_variant 0.12
rpoB 761301 p.Arg499Gly missense_variant 0.12
rpoB 762724 p.Gly973Ala missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765846 p.Asn826Ile missense_variant 0.15
rpoC 766823 p.Lys1152Glu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777457 p.Gly342Arg missense_variant 0.22
mmpS5 779490 c.-585T>A upstream_gene_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800648 c.-161A>G upstream_gene_variant 0.12
Rv1258c 1406668 p.Leu225Met missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.18
rrl 1474556 n.899G>T non_coding_transcript_exon_variant 0.17
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.12
rrl 1475727 n.2070C>T non_coding_transcript_exon_variant 0.12
rrl 1476147 n.2490G>C non_coding_transcript_exon_variant 0.14
inhA 1673724 c.-478A>T upstream_gene_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918284 c.345C>T synonymous_variant 0.18
tlyA 1918700 p.Lys254Arg missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 0.95
katG 2155294 p.Gly273Asp missense_variant 0.13
katG 2155661 p.Val151Phe missense_variant 0.14
katG 2155923 c.189C>T synonymous_variant 0.14
katG 2155940 p.Met58Val missense_variant 0.14
katG 2156104 p.Glu3Val missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 0.95
PPE35 2169632 c.981C>T synonymous_variant 0.2
PPE35 2169641 c.972G>A synonymous_variant 0.15
PPE35 2170104 p.Leu170Pro missense_variant 0.11
PPE35 2170241 c.372C>T synonymous_variant 0.12
PPE35 2170419 p.Met65Lys missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289699 c.-458T>C upstream_gene_variant 0.11
pncA 2289851 c.-610A>G upstream_gene_variant 0.13
pncA 2289878 c.-637C>T upstream_gene_variant 0.14
kasA 2518105 c.-10C>G upstream_gene_variant 0.12
kasA 2518115 p.Val1Leu missense_variant 0.13
ahpC 2726394 p.Phe68Leu missense_variant 0.12
ahpC 2726584 p.Ala131Val missense_variant 0.13
folC 2746595 c.1003delA frameshift_variant 0.12
folC 2747119 p.Phe160Leu missense_variant 0.12
folC 2747337 p.Ala88Thr missense_variant 0.22
pepQ 2859492 c.927G>A synonymous_variant 0.12
pepQ 2860319 p.Ser34Pro missense_variant 0.12
ribD 2987336 c.498C>A synonymous_variant 0.13
ribD 2987381 c.543G>A synonymous_variant 0.14
ribD 2987419 p.Gly194Asp missense_variant 0.18
Rv2752c 3066187 p.Asp2Gly missense_variant 0.11
thyX 3067803 p.Ser48Phe missense_variant 0.12
thyX 3067921 p.Val9Met missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086831 c.12T>C synonymous_variant 0.12
Rv3083 3449398 p.Ala299Pro missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474989 p.Pro328Leu missense_variant 0.15
fprA 3475307 p.Gly434Asp missense_variant 0.13
Rv3236c 3612564 p.Met185Leu missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 0.93
fbiB 3640920 c.-615A>G upstream_gene_variant 0.1
alr 3840599 c.822G>A synonymous_variant 0.12
alr 3841250 c.171C>T synonymous_variant 0.15
rpoA 3878480 p.Ser10Pro missense_variant 0.14
clpC1 4038268 p.Gly813Cys missense_variant 0.22
clpC1 4038444 p.Ala754Val missense_variant 0.14
clpC1 4039109 c.1596C>T synonymous_variant 0.14
clpC1 4040491 p.Gln72* stop_gained 0.14
panD 4044340 c.-59G>A upstream_gene_variant 0.18
embC 4239797 c.-66G>T upstream_gene_variant 0.22
embC 4240521 p.Thr220Ile missense_variant 0.13
embC 4240534 c.672C>T synonymous_variant 0.14
embC 4240606 c.744G>A synonymous_variant 0.13
embC 4242176 p.Pro772Ser missense_variant 0.13
embA 4242559 c.-674G>A upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243000 c.-233C>G upstream_gene_variant 0.12
embC 4243015 p.Asp1051Glu missense_variant 0.14
embC 4243023 p.Phe1054Ser missense_variant 0.12
embC 4243029 p.Asp1056Gly missense_variant 0.13
embA 4243036 c.-197C>T upstream_gene_variant 0.25
embA 4243386 p.Asp52Asn missense_variant 0.15
embA 4243457 c.225C>T synonymous_variant 0.13
embA 4243460 c.228C>T synonymous_variant 0.87
embA 4243485 p.Asn85Asp missense_variant 0.11
embA 4245557 p.Glu775Asp missense_variant 0.13
embB 4246493 c.-21A>G upstream_gene_variant 0.11
embB 4246519 c.6A>G synonymous_variant 0.11
embB 4247357 p.Val282Met missense_variant 0.15
embB 4248221 p.Pro570Ser missense_variant 0.12
embB 4249371 p.Leu953Pro missense_variant 0.13
embB 4249608 p.Thr1032Ile missense_variant 0.14
aftB 4267619 c.1218C>T synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.92
aftB 4267661 c.1176G>A synonymous_variant 0.15
aftB 4268381 p.Trp152* stop_gained 0.15
aftB 4268450 c.387A>G synonymous_variant 0.2
ubiA 4269472 p.Thr121Ser missense_variant 0.15
aftB 4269795 c.-959G>A upstream_gene_variant 0.17
whiB6 4338460 p.Met21Thr missense_variant 0.18
whiB6 4338471 p.Arg17Ser missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.97